| Variant ID: vg1126363345 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26363345 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGCAGATTGAGATGGTGGTTTCCCCCACCATCTGCAATGTGAAGTTGGGGCGTGTCCTCATAGATGGAGGAGCGGCTCTCAACATCCTTTCCCCCGCGGC[C/T]
TTTGATGCTATCAAGGCCCCGGGGATGGTGCTCCAGCCGTCTCAACCGATCATTGGTGTGACGCCGGGGCACACATGGCCGTTAGGTCACATCGACCTAC
GTAGGTCGATGTGACCTAACGGCCATGTGTGCCCCGGCGTCACACCAATGATCGGTTGAGACGGCTGGAGCACCATCCCCGGGGCCTTGATAGCATCAAA[G/A]
GCCGCGGGGGAAAGGATGTTGAGAGCCGCTCCTCCATCTATGAGGACACGCCCCAACTTCACATTGCAGATGGTGGGGGAAACCACCATCTCAATCTGCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.70% | 0.10% | 21.65% | 57.60% | NA |
| All Indica | 2759 | 8.10% | 0.00% | 19.83% | 72.09% | NA |
| All Japonica | 1512 | 41.10% | 0.30% | 21.76% | 36.90% | NA |
| Aus | 269 | 28.30% | 0.00% | 35.32% | 36.43% | NA |
| Indica I | 595 | 5.20% | 0.00% | 8.74% | 86.05% | NA |
| Indica II | 465 | 4.50% | 0.00% | 12.47% | 83.01% | NA |
| Indica III | 913 | 8.70% | 0.00% | 31.54% | 59.80% | NA |
| Indica Intermediate | 786 | 11.70% | 0.00% | 18.96% | 69.34% | NA |
| Temperate Japonica | 767 | 45.80% | 0.00% | 7.82% | 46.41% | NA |
| Tropical Japonica | 504 | 30.40% | 0.60% | 41.87% | 27.18% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.40% | 24.07% | 26.97% | NA |
| VI/Aromatic | 96 | 37.50% | 0.00% | 33.33% | 29.17% | NA |
| Intermediate | 90 | 23.30% | 0.00% | 22.22% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126363345 | C -> T | LOC_Os11g43670.1 | synonymous_variant ; p.Ala642Ala; LOW | synonymous_codon | Average:6.564; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1126363345 | C -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:6.564; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |